[English] 日本語
Yorodumi
- PDB-4zos: 2.20 Angstrom resolution crystal structure of protein YE0340 of u... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zos
Title2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081]
Componentsprotein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Yersinia enterocolitica subsp. enterocolitica 8081 / hypothetical protein YE0340 / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHalavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081]
Authors: Halavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
B: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
C: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
D: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2536
Polymers49,0644
Non-polymers1902
Water1,33374
1
C: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
D: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6273
Polymers24,5322
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-26 kcal/mol
Surface area10490 Å2
MethodPISA
2
A: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
B: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6273
Polymers24,5322
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-27 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.675, 37.135, 82.583
Angle α, β, γ (deg.)87.66, 88.25, 61.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA6 - 1019 - 104
21SERSERVALVALBB6 - 1019 - 104
12METMETSERSERAA1 - 1024 - 105
22METMETSERSERCC1 - 1024 - 105
13SERSERSERSERAA6 - 1029 - 105
23SERSERSERSERDD6 - 1029 - 105
14SERSERVALVALBB6 - 1019 - 104
24SERSERVALVALCC6 - 1019 - 104
15SERSERVALVALBB6 - 1019 - 104
25SERSERVALVALDD6 - 1019 - 104
16SERSERSERSERCC6 - 1029 - 105
26SERSERSERSERDD6 - 1029 - 105

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081


Mass: 12265.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Yersinia enterocolitica subsp. enterocolitica 8081 / Plasmid: pMCSG7-Halo / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A0A0M3KL35*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Crystallization: 20%Polyethylene Glycol 8000, 0.2M Sodium Chloride,Phosphate-Citrate Protein at 20 mg/ml

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2015
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 18325 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.2 / % possible all: 90

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X7V

1x7v


Resolution: 2.2→29.66 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.299 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28529 931 5.1 %RANDOM
Rwork0.22883 ---
obs0.23165 17175 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.256 Å2
Baniso -1Baniso -2Baniso -3
1--18.95 Å21.75 Å212.1 Å2
2---9.65 Å2-6.08 Å2
3---28.6 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 10 74 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193400
X-RAY DIFFRACTIONr_bond_other_d0.0050.023193
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9794627
X-RAY DIFFRACTIONr_angle_other_deg1.18537387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5695408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.61924.535172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.59915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1211525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213808
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55220.13
12B55220.13
21A60540.09
22C60540.09
31A54870.13
32D54870.13
41B53920.14
42C53920.14
51B57330.09
52D57330.09
61C54210.14
62D54210.14
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 76 -
Rwork0.264 1167 -
obs--90.6 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more